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Topyfic

Topyfic: Reproducible latent dirichlet allocation (LDA) using leiden clustering and harmony for single cell epigenomics data

An open challenge for the analysis of single-cell data is the identification of distinct cellular programs that may be simultaneously expressed in the same cell based on the interaction of genotypes in environments. Latent Dirichlet allocation (LDA) is a popular statistical method for the identification of recurring patterns in count data (e.g. gene expression), which are referred to as topics. These topics are composed of genes with specific weights that can together explain underlying patterns of gene expression profile for each individual cell. In particular, each cell’s expression profile can be decomposed into a combination of the topics that can be analyzed both globally using topic-trait enrichment as well as in individual cells using structure plots. Due to the random initialization of LDA algorithms, topic definitions can vary substantially each time that the algorithm is rerun, which hinders their interpretability. Therefore, we developed reproducible LDA where we define our topics by analysing their reproducibility across a large number of runs.

Topyfic is a Python library designed to apply rLDA to single_cells/bulk RNA-seq data to recover meaningful topics that involve the key genes like transcription factors involved in different steps.

LDA overview

Topyfic overview

Documentation

Topyfic's full documentation can be found at here

Installation

To install Topyfic, python version 3.9 or greater is required.

IMPORTANT: If you upgrade Topyfic from any version below 0.4.5 you need to run this

import Topyfic
#read your top model
top_model = Topyfic.read_topModel(FILE_NAME)
top_model.model = top_model.rLDA
top_model.save_topModel()

Install from PyPi (recommended)

Install the most recent release, run

pip install Topyfic

Install with the most recent commits

git cloning the Topyfic repository, going to the Topyfic directory, run

pip install .

Tutorials

In general, you need to make three objects (Train, TopModel and Analysis).

Topyfic workflow

The Train object can be initialized either from (a) single cell RNA-seq dataset or (b) single cell ATAC-seq or (c) bulk RNA-seq.

Training part can be time-consuming depending on how big your data is, however you can learn each train model per random state in different jobs and then combine all together. Look at this tutorial for mor information.

For guidance on using Topyfic to analyze your data look at our more depth-in tutorials:

Analysing single cell C2C12 data only using regulatory elements: Analysing single cell and single nucleus using C2C12 ENCODE datasets using regulatory elements instead of all genes.
Analysing single cell microglia data: Analysing single cell microglia data from Model-AD portal.
Analysing ENCODE time course hippocampus data: Analysing parse single-nucleus RNA-seq data and RNA part of 10x multiome hippocampus data from ENCODE.

If you are using other methods to learn your topics, but you are still interested in doing downstream analysis, you can embeded your results in the format describe here. Once you have all your files ready you can embed them Topyfic format following the instruction in the same tutorial.

Snakemake workflow

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.

To focus more deeply on downstream analyses, I provide a Snakemake workflow to train and build three necessary objects (Train, TopModel, and Analysis).

For more information on how to run Topyfic Snakemake, please look here.

Cite

Please cite our paper when using Topyfic:

Topyfic

@article{rezaie2024identification,
  title={Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD},
  author={Rezaie, Narges and Rebboah, Elisabeth and Williams, Brian A and Liang, Heidi Yahan and Reese, Fairlie and Balderrama-Gutierrez, Gabriela and Dionne, Louise and Reinholdt, Laura G and Trout, Diane and Wold, Barbara and others},
  journal={bioRxiv},
  pages={2024--02},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}